/trunk Developers: msuchard

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msuchard 2013-05-09 01:55 Rev.: 5640

Fixing TreeTransform applied to EmpiricalTreeDistribution (again)

6 lines of code changed in 6 files:

• src/dr/evomodel/tree: ProgressiveScalarTreeTransform.java (+2 -2), SingleScalarTreeTransform.java (new), TreeTransform.java (+2 -1)

msuchard 2013-05-08 07:20 Rev.: 5638

Incorrectly delegated getBranchLength() such that no transformation was occurring.

17 lines of code changed in 5 files:

• src/dr/evomodel/tree: ProgressiveScalarTreeTransform.java (+2 -2), SingleScalarTreeTransform.java (+2 -2), TransformedTreeModel.java (+11 -7), TreeTransform.java (+2 -2)

msuchard 2013-05-08 04:03 Rev.: 5637

Updated MultivariateTraitTree to work with EmpiricalTreeDistribution

10 lines of code changed in 5 files:

• src/dr/evolution/tree: MultivariateTraitTree.java (-3)
• src/dr/evomodel/tree: ProgressiveScalarTreeTransform.java (+1 -1), SingleScalarTreeTransform.java (+2 -2), TransformedTreeModel.java (+7 -4)

msuchard 2013-05-07 07:43 Rev.: 5635

Fixing transformed trees when random

404 lines of code changed in 21 files:

• src/dr/evolution/tree: MultivariateTraitTree.java (+7 -1)
• src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+4 -4), FullyConjugateMultivariateTraitLikelihood.java (new), IntegratedMultivariateTraitLikelihood.java (+2 -3), MissingTraits.java (new), MultinomialLatentLiabilityLikelihood.java (+25 -1), NonPhylogeneticMultivariateTraitLikelihood.java (new), OrderedLatentLiabilityLikelihood.java (+25 -1), SampledMultivariateTraitLikelihood.java (+27 -1), SemiConjugateMultivariateTraitLikelihood.java (new)
• src/dr/evomodel/tree: ProgressiveScalarTreeTransform.java (+3 -2), TransformedTreeModel.java (+246 -7)
• src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+27 -2)

msuchard 2013-05-06 15:27 Rev.: 5631

Finally interfacing multivariate traits, although they are now generally integrated out.

265 lines of code changed in 17 files:

• src/dr/evolution/tree: MultivariateTraitTree.java (+35)
• src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (+10 -14), DiffusionRateStatistic.java (+33 -7), IntegratedMultivariateTraitLikelihood.java (+3 -2)
• src/dr/evomodel/operators: DiscretizedLocationOperator.java (new), LatentLiabilityGibbsOperator.java (new), PrecisionMatrixGibbsOperator.java (new), TraitGibbsOperator.java (new), TraitRateGibbsOperator.java (new)
• src/dr/evomodel/tree: TreeModel.java (+64 -64)

msuchard 2013-05-03 07:25 Rev.: 5628

Fixed log determine of a matrix and positive-definite check in WishartDistribution; there is still an error in LUPDecomposition.isPD()

21 lines of code changed in 6 files:

• src/dr/app/beast: release_parsers.properties (new)
• src/dr/math/distributions: WishartDistribution.java (+5 -7)
• src/dr/math/matrixAlgebra: LUPDecomposition.java (+15 -5)

msuchard 2013-04-29 03:42 Rev.: 5619

Added missing CompoundParameter.fireParameterChangedEvent method, and demonstrating a nicer approach to multi-developer debugging.

33 lines of code changed in 4 files:

• src/dr/inference/model: CompoundParameter.java (+5)
• src/dr/inference/operators: AdaptableVarianceMultivariateNormalOperator.java (+28 -14)

msuchard 2013-04-28 06:43 Rev.: 5617

Stream-lining serial operations during multi-parameter updates

49 lines of code changed in 3 files:

• src/dr/inference/model: Parameter.java (+17 -15)
• src/dr/inference/operators: AdaptableVarianceMultivariateNormalOperator.java (+32 -15)

msuchard 2013-04-25 06:38 Rev.: 5610

Implemented a scaled mixture of Wishart distribution for precision matrix inference.

444 lines of code changed in 12 files:

• src/dr/app/beast: development_parsers.properties (+2)
• src/dr/evomodel/operators: PrecisionMatrixGibbsOperator.java (+78 -20)
• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (new), WishartGammalDistributionModel.java (new 183)
• src/dr/inferencexml/distribution: WishartGammaDistributionModelParser.java (new 95)
• src/dr/math/distributions: HalfTDistribution.java (new), InverseWishartDistribution.java (+29 -4), WishartDistribution.java (+2 -6), WishartStatistics.java (new 39)

msuchard 2013-04-23 14:39 Rev.: 5602

Added a half-T-distribution for more flexible specification of precision matrices in trait evolution.

189 lines of code changed in 3 files:

• src/dr/inferencexml/distribution: PriorParsers.java (+136 -92)
• src/dr/math/distributions: HalfTDistribution.java (+53)

msuchard 2013-04-19 06:30 Rev.: 5599

Debugging flag to check for thread-level parallelization of likelihood evaluations

15 lines of code changed in 4 files:

• src/dr/app/beagle/evomodel/treelikelihood: AbstractTreeLikelihood.java (+5 -5)
• src/dr/inference/model: CompoundLikelihood.java (+10 -1)

msuchard 2013-04-18 08:47 Rev.: 5594

Reimplemented lazy evaluation in Skygrid and cleaned up formatting.

497 lines of code changed in 4 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (new), GMRFSkyrideLikelihood.java (+275 -273)

msuchard 2013-04-16 07:24 Rev.: 5592

Changing default behaviour to original.

3 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/parsers: ComplexSubstitutionModelParser.java (+3 -3)

msuchard 2013-04-16 07:21 Rev.: 5591

Passing eigendecomposition condition number checking up to XML level.

25 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/parsers: ComplexSubstitutionModelParser.java (+25 -7)

msuchard 2013-04-15 09:25 Rev.: 5590

Fixed Jacobian for log-transforms under new adaptive multivariate transition kernel for mixture models.

4 lines of code changed in 4 files:

• src/dr/app/beast: development_parsers.properties (+1 -1)
• src/dr/inference/operators: AdaptableVarianceMultivariateNormalOperator.java (+2)
• src/dr/util: Transform.java (+1 -1)

msuchard 2013-04-06 05:50 Rev.: 5561

Example of logging

41 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+41)

msuchard 2013-04-06 05:29 Rev.: 5560

Example of lazy evaluation after tree change events.

27 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+27 -3)

msuchard 2013-04-06 05:11 Rev.: 5559

Reconstructions from AncestralStateBeagleTreeLikelihood now follow useAmbiguities=true/false setting.

26 lines of code changed in 6 files:

• src/dr/app/beagle/evomodel/substmodel: ComplexSubstitutionModel.java (+17 -6)
• src/dr/app/beagle/evomodel/treelikelihood: AncestralStateBeagleTreeLikelihood.java (+2 -2), BeagleTreeLikelihood.java (+7)

msuchard 2013-03-27 06:44 Rev.: 5545

Fixed memory allocation bug introduced in previous commit.

1 lines of code changed in 2 files:

• src/dr/inference/model: DiagonalMatrix.java (new)

msuchard 2013-03-27 03:48 Rev.: 5544

Implemented a log-determinant routine for numerical stability and fixed getParameterValue in DiagonalMatrix

857 lines of code changed in 5 files:

• src/dr/inference/model: DiagonalMatrix.java (+58 -25)
• src/dr/math/distributions: WishartDistribution.java (+31 -5)
• src/dr/math/matrixAlgebra: LUPDecomposition.java (+278 -268), Matrix.java (new)

(700 more)